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TimiRGeN

This is the development version of TimiRGeN; for the stable release version, see TimiRGeN.

Time sensitive microRNA-mRNA integration, analysis and network generation tool


Bioconductor version: Development (3.19)

TimiRGeN (Time Incorporated miR-mRNA Generation of Networks) is a novel R package which functionally analyses and integrates time course miRNA-mRNA differential expression data. This tool can generate small networks within R or export results into cytoscape or pathvisio for more detailed network construction and hypothesis generation. This tool is created for researchers that wish to dive deep into time series multi-omic datasets. TimiRGeN goes further than many other tools in terms of data reduction. Here, potentially hundreds-of-thousands of potential miRNA-mRNA interactions can be whittled down into a handful of high confidence miRNA-mRNA interactions affecting a signalling pathway, across a time course.

Author: Krutik Patel [aut, cre]

Maintainer: Krutik Patel <nkp68 at newcastle.ac.uk>

Citation (from within R, enter citation("TimiRGeN")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("TimiRGeN")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("TimiRGeN")
TimiRGeN HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Clustering, Network, Pathways, Software, TimeCourse, Visualization, miRNA
Version 1.13.3
In Bioconductor since BioC 3.12 (R-4.0) (3.5 years)
License GPL-3
Depends R (>= 4.3), Mfuzz, MultiAssayExperiment
Imports biomaRt, clusterProfiler, dplyr (>= 0.8.4), FreqProf, gtools (>= 3.8.1), gplots, ggdendro, gghighlight, ggplot2, graphics, grDevices, igraph (>= 1.2.4.2), RCy3, readxl, reshape2, rWikiPathways, scales, stats, tidyr (>= 1.0.2), stringr (>= 1.4.0)
System Requirements
URL https://github.com/Krutik6/TimiRGeN/
Bug Reports https://github.com/Krutik6/TimiRGeN/issues
See More
Suggests BiocManager, kableExtra, knitr (>= 1.27), org.Hs.eg.db, org.Mm.eg.db, testthat, rmarkdown
Linking To
Enhances
Depends On Me
Imports Me
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Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package TimiRGeN_1.13.3.tar.gz
Windows Binary TimiRGeN_1.13.3.zip
macOS Binary (x86_64) TimiRGeN_1.13.3.tgz
macOS Binary (arm64) TimiRGeN_1.13.3.tgz
Source Repository git clone https://git.bioconductor.org/packages/TimiRGeN
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/TimiRGeN
Bioc Package Browser https://code.bioconductor.org/browse/TimiRGeN/
Package Short Url https://bioconductor.org/packages/TimiRGeN/
Package Downloads Report Download Stats